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#include "../algorithms/antennaselector.h"
#include "../algorithms/baselineselector.h"
#include "../structures/msmetadata.h"
#include "../quality/defaultstatistics.h"
#include "../quality/histogramcollection.h"
#include "../quality/qualitytablesformatter.h"
#include "../quality/statisticscollection.h"
#include "../quality/statisticsderivator.h"
#include "../quality/histogramtablesformatter.h"
#include <casacore/ms/MeasurementSets/MeasurementSet.h>
#include <casacore/tables/Tables/ArrayColumn.h>
#include <casacore/tables/Tables/ScalarColumn.h>
#include <iostream>
using algorithms::AntennaSelector;
using algorithms::BaselineSelector;
StatisticsCollection load(const std::string& filename,
std::vector<AntennaInfo>& antennae) {
StatisticsCollection statisticsCollection;
const HistogramCollection histogramCollection;
const MSMetaData ms(filename);
const unsigned polarizationCount = ms.PolarizationCount();
statisticsCollection.SetPolarizationCount(polarizationCount);
QualityTablesFormatter qualityData(filename);
statisticsCollection.Load(qualityData);
const unsigned antennaCount = ms.AntennaCount();
for (unsigned a = 0; a < antennaCount; ++a)
antennae.push_back(ms.GetAntennaInfo(a));
return statisticsCollection;
}
std::set<size_t> detectRFIPercentage(const char* filename) {
std::vector<AntennaInfo> antennae;
StatisticsCollection statisticsCollection = load(filename, antennae);
BaselineSelector selector;
selector.SetUseLog(true);
statisticsCollection.IntegrateBaselinesToOneChannel();
const BaselineStatisticsMap& baselineMap =
statisticsCollection.BaselineStatistics();
const std::vector<std::pair<unsigned, unsigned>> list =
baselineMap.BaselineList();
for (std::vector<std::pair<unsigned, unsigned>>::const_iterator i =
list.begin();
i != list.end(); ++i) {
const unsigned a1 = i->first, a2 = i->second;
DefaultStatistics statistic = baselineMap.GetStatistics(a1, a2);
selector.Add(statistic, antennae[a1], antennae[a2]);
}
std::vector<BaselineSelector::SingleBaselineInfo> markedBaselines;
std::set<unsigned> badStations;
selector.Search(markedBaselines);
selector.ImplyStations(markedBaselines, 0.3, badStations);
std::cout << "List of " << badStations.size() << " bad stations:\n";
for (const size_t ant : badStations) {
std::cout << antennae[ant].name << " (" << ant << ")\n";
}
return std::set<size_t>(badStations.begin(), badStations.end());
}
std::set<size_t> detectStddev(const char* filename) {
std::vector<AntennaInfo> antennae;
const StatisticsCollection statisticsCollection = load(filename, antennae);
AntennaSelector selector;
std::vector<size_t> badStations = selector.Run(statisticsCollection);
std::cout << "List of " << badStations.size() << " bad stations:\n";
for (const size_t ant : badStations) {
std::cout << antennae[ant].name << " (" << ant << ")\n";
}
return std::set<size_t>(badStations.begin(), badStations.end());
}
void flagAntennas(const char* filename, const std::set<size_t>& antennae) {
casacore::MeasurementSet ms(filename, casacore::Table::Update);
/**
* Read some meta data from the measurement set
*/
const casacore::MSSpectralWindow spwTable = ms.spectralWindow();
const size_t spwCount = spwTable.nrow();
if (spwCount != 1)
throw std::runtime_error("Set should have exactly one spectral window");
const casacore::ScalarColumn<int> numChanCol(
spwTable, casacore::MSSpectralWindow::columnName(
casacore::MSSpectralWindowEnums::NUM_CHAN));
const size_t channelCount = numChanCol.get(0);
if (channelCount == 0) throw std::runtime_error("No channels in set");
const casacore::ScalarColumn<int> ant1Column(
ms, ms.columnName(casacore::MSMainEnums::ANTENNA1));
const casacore::ScalarColumn<int> ant2Column(
ms, ms.columnName(casacore::MSMainEnums::ANTENNA2));
casacore::ArrayColumn<bool> flagsColumn(
ms, ms.columnName(casacore::MSMainEnums::FLAG));
if (ms.nrow() == 0) throw std::runtime_error("Table has no rows (no data)");
const casacore::IPosition flagsShape = flagsColumn.shape(0);
const casacore::Array<bool> flags(flagsShape, true);
std::cout << "Flagging... " << std::flush;
/**
* Flag
*/
size_t crossCount = 0, autoCount = 0;
for (size_t rowIndex = 0; rowIndex != ms.nrow(); ++rowIndex) {
// Selected?
if (antennae.find(ant1Column.get(rowIndex)) != antennae.end() ||
antennae.find(ant2Column.get(rowIndex)) != antennae.end()) {
if (ant1Column.get(rowIndex) == ant2Column.get(rowIndex))
++autoCount;
else
++crossCount;
flagsColumn.put(rowIndex, flags);
}
}
std::cout << "DONE (selected " << crossCount << " cross- and " << autoCount
<< " auto-correlated timesteps)\n";
}
void printSyntax(std::ostream& stream, char* argv[]) {
stream << "The executable 'badstations' will give a list of stations that "
"are outliers\n"
"according to the RFI statistics.\n"
"\n"
"Syntax: badstations [options] <filename>\n"
"\n"
"Options:\n"
"-flag\n"
" Will not only show statistics, but also flag the antennas that "
"are found\n"
" to be bad in the measurement set.\n"
" (this only works if the given filename is a measurement set, "
"not a .ref).\n"
"-method <stddev / percentage>\n"
" Select detection method. Method 'stddev' is the default, and "
"simply detects\n"
" stations with an outlyer standard deviation. Method "
"'percentage' detects\n"
" outliers based on the percentage RFI statistic, taking into "
"account that\n"
" short baselines often see fewer RFI, by fitting a curve to the "
"statistic\n"
" as a function of baseline.\n";
}
int main(int argc, char* argv[]) {
#ifdef HAS_LOFARSTMAN
register_lofarstman();
#endif // HAS_LOFARSTMAN
int argi = 1;
bool doFlag = false;
enum Method { StddevMethod, RFIPercentangeMethod } method = StddevMethod;
while (argi < argc && argv[argi][0] == '-') {
const std::string p(argv[argi] + 1);
if (p == "flag") {
doFlag = true;
} else if (p == "method") {
++argi;
const std::string m = argv[argi];
if (m == "stddev")
method = StddevMethod;
else if (m == "percentage")
method = RFIPercentangeMethod;
else
throw std::runtime_error("Unknown method given");
} else {
throw std::runtime_error("Unknown parameter");
}
++argi;
}
if (argi >= argc) {
printSyntax(std::cerr, argv);
return -1;
} else {
const char* filename = argv[argi];
std::set<size_t> badAntennas;
switch (method) {
case StddevMethod:
badAntennas = detectStddev(filename);
break;
case RFIPercentangeMethod:
badAntennas = detectRFIPercentage(filename);
break;
}
if (doFlag) flagAntennas(filename, badAntennas);
return 0;
}
}
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